The official at the heart of the Clinton email "quid pro quo" controversy broke his silence Tuesday saying "his motivations were never political."

U.S. State Department's Under Secretary of State for Management, Patrick Kennedy said in a statement to NBC News and other media outlets that he reached out the FBI last year to understand why a Clinton email was upgraded to classified status, not to bargain to change that classification.

The State Department came under scrutiny after the FBI released documents which showed that a bureau employee claimed a colleague had discussed some sort of bargain with a high level State Department official over former Secretary of State Hillary Clinton's email. NBC News has not authenticated any of the alleged e-mails nor had the Clinton campaign.

Hillary Clinton gives an economic speech at New York University on July 24, 2015 in New York City.Spencer Platt / Getty Images

Kennedy, the State Department official in question, discredited any such assertion.

"There was no quid pro quo, nor was there any bargaining. At no point in our conversation was I under the impression we were bargaining," Kennedy told NBC News.

It appears the exchange between both agencies took place over two separate conversations.

The first involved Kennedy contacting an FBI official, who was named by the Washington Post as Brian McCauley, about the classification of a single email that was in dispute. The second, was between McCauley and a bureau employee whose job involved classification review.

McCauley had been trying to reach Kennedy about the issue of office space for agents in overseas embassies and consulates because he had a say in allocating space at diplomatic outposts. After Kennedy raised the issue of classification, McCauley raised the issue of office space, according to the FBI document.

That is when things got murky for McCauley who appeared to offer what another FBI employee later described as "quid pro quo."

“He had a request. I found out what the request was for. I absolutely said emphatically I would not support it,” McCauley said in an extensive interview with the Washington Post.

But Kennedy vehemently denies that the "two matters" were "linked."

"We take very seriously our responsibility to decide whether our documents are classified or not classified. We can’t simply cede that responsibility to another agency, as it is my signature or one of my senior officers' signature which goes on the classification action and it is the State Department which must prepare the legal justification if we are challenged in court," he said.

And the State Department is backing him up.

Undersecretary of State for Management Patrick Kennedy testifies Sept. 8 before the House Oversight and Government Reform Committee in Washington.Molly Riley / AP

State Department spokesman Mark Toner, at a press briefing on Tuesday, said there was “nothing out of line” with Kennedy calling the FBI to argue against their desire to upgrade the classification of an email, .

The conversation was to make sure all classifications were appropriately upgraded, he said.

"We did look at what areas or portions or parts of these emails should be redacted and we wanted to make certain that there was a solid rationale, legally and otherwise behind these upgrades," he said.

The State Department always wanted to comply with Freedom of Information Act requests and "make as much public" as they could, he said.

Ultimately, the State Department upgraded the email to "secret." No increase in the FBI's slots in Baghdad resulted from the conversation, and the FBI ordered a review of the conduct of the now-retired FBI official.

But that didn't stop Clinton's presidential rival Donald Trump from swiftly jumping on the controversy.

"The news that top Clinton aide Patrick Kennedy tried to engage in a blatant quid pro quo for changing the classification level of several of Clinton's emails shows a cavalier attitude towards protecting our nation's secrets," Trump spokesman Jason Miller said in a statement.

"Kennedy must resign from the State Department immediately and Clinton must state he has no place in her administration if she is elected President."